CMAPCollection
,
GeneSet
, or
GeneSetCollection
object containing the 'query'
gene sets to compare against the 'sets'CMAPCollection
,
GeneSetCollection
or
GeneSet
objectinduceCMAPCollection
.induceCMAPCollection
.induceCMAPCollection
.induceCMAPCollection
needs to contain to be included in the analysis (Default:5).signature(query = "CMAPCollection", sets = "CMAPCollection", universe = "character")
signature(query = "CMAPCollection", sets = "NChannelSet", universe = "character")
signature(query = "SignedGeneSet", sets = "CMAPCollection", universe = "character")
signature(query = "SignedGeneSet", sets = "NChannelSet", universe = "character")
signature(query = "GeneSet", sets = "CMAPCollection", universe = "character")
signature(query = "GeneSet", sets = "NChannelSet", universe = "character")
signature(query = "GeneSetCollection", sets = "CMAPCollection", universe = "character")
signature(query = "GeneSetCollection", sets = "NChannelSet", universe = "character")
signature(query = "GeneSet", sets = "GeneSetCollection", universe = "character")
signature(query = "CMAPCollection", sets = "GeneSetCollection", universe = "character")
signature(query = "GeneSetCollection", sets = "GeneSetCollection", universe = "character")
signature(query = "GeneSet", sets = "GeneSet", universe = "character")
fisher.test
data(gCMAPData)
gene.set.collection <- induceCMAPCollection(gCMAPData, "z", higher=2, lower=-2)
## compare all gene sets in the gene.set.collection to each other
universe = featureNames(gCMAPData)
fisher_score(gene.set.collection, gene.set.collection, universe = universe)
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